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The name Brantham is of Anglo Saxon origin - Brant for 'hill' and ham 'village' — hence, 'village on the hill'. Another possible translation may be 'burnt village', a name given after a Viking invasion coming up from the River Stour. Evidence of the village's Saxon hertigae can be found in the form of some silver ninety coins from the time of Edward the Elder (899-924) in what has become known as the Brantham Hoard, found in the village in 2003.

Brantham is mentioned in the 1086 Domesday book as having 38 households and under the lordship of Aelfric of Weinhou. Until 1887 the local economy was almost entirely agricultural. This changed in 1887 when British Xylonite Ltd. purchased the 130-acre (0.53 km2) Brooklands Farm and built their factory, which was later renamed BX Plastics.[2] There was insufficient accommodation available locally for the workforce, so the company also built Brantham New Village, consisting of about 60 new houses.

Brantham's parish church of St. Michael and All Angels dates back to the 14th century, although it is believed a religious building has been on the site for over 1,000 years. The church also has connections with Dodnash Priory (founded in 1188). When the priory was dissolved at the time of the Reformation, it is thought that some of the priory's medieval glass was fitted in one of the south facing nave windows. The church underwent extensive repairs in 2004 following extensive fund raising efforts and a £23,000 grant from the UK National Lottery. St Michael's owns one of only two known religious paintings by John Constable. "Christ blessing the children" was presented to the church by the artist himself in 1805. A reproduction hangs on display in the church today but the original is kept at the Ipswich museum. Brantham is generally acknowledged, along with Flatford, Dedham and East Bergholt, to be part of 'Constable Country'. The artist chose a cottage in the village overlooking the Stour as a subject to one of his sketches 'Fisherman's cottage in Brantham with a view of Mistley Hall' in 1796. The drawing, which is in the V&A museum in London is one of the earliest dated drawings by Constable of which the whereabouts are now known.

The Tudor didactic poet Thomas Tusser settled at Katwade (now Cattawade) and is believed to have written his most famous work "A Hundreth Good Pointes of Husbandrie" at Braham Hall. The lord of the manor of Brantham in the 15th century was 'shire knight of Suffolk' Sir John Braham (d.1420).

The village's oldest pub, the Brantham Bull, is a 16th-century grade 2 listed building. Some of the beams from the building are thought to have come from the wreckage of the Spanish armarda and over the centuries the building has also been used as a court house and a prison. Witchfinder general Matthew Hopkins, once hanged a lady by the name of Nancy on the green outside the front of the building. A passage used by smugglers used to run from the pub's cellar out to the River Stour.

Brantham is about half a mile from Manningtree station. A long railway cutting runs past the village. At one point near Brantham Bull it is the deepest railway cutting in Suffolk. There was once a siding to Marsh Farm, where fresh fruit and vegetables were loaded for London, and a siding going into the old BX Plastics factory (now derelict) for loading and unloading materials. Both were disused by the end of the 1930s.